Commit 98aac765 authored by Meike Klischies's avatar Meike Klischies

Merge remote-tracking branch 'origin/master'

parents c218ba3c cac175d8
......@@ -76,7 +76,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 8,
"metadata": {},
"outputs": [
{
......@@ -91,17 +91,24 @@
"source": [
"# enter dive number\n",
"dive = \"0XXX\"\n",
"device = \"Abyss\"\n",
"\n",
"# set name of this jupyter notebook file\n",
"# if this file is not in your working directory, specify the whole file path\n",
"notebook = \"/path/to/notebook/AUVAbyssWorkflow_singlesurvey_MK.ipynb\"\n",
"\n",
"# enter spatial resolution in meter\n",
"sr = 3\n",
"\n",
"# enter rootpath of raw-data\n",
"rootpath = \"/media/jochen/Work/AUV_navadjust_4Jochen/Abyss0253\"\n",
"rootpath = \"path/to/data/Abyss0253\"\n",
"\n",
"print (dive)\n",
"print (sr)\n",
"\n",
"# define mbsystem internal file ending\n",
"file_ending = \".mb88\"\n",
"\n",
"# define names of datalists\n",
"datalistraw = \"datalistraw_\" + str(dive) + \".mb-1\"\n",
"datalistp = \"datalistp_\" + str(dive) + \".mb-1\"\n",
......@@ -109,12 +116,12 @@
"datalistppp = \"datalistppp_\" + str(dive) + \".mb-1\"\n",
"\n",
"# define names of grids\n",
"grd1 = \"Abyss_\" + str(dive) + \"_raw_\" + str(sr) + \"m\"\n",
"grd1nav = \"Abyss_\" + str(dive) + \"_raw_nav\"\n",
"grd2arcAscii = \"Abyss_\" + str(dive) + \"_navadj_\" + str(sr) + \"m_arcAscii\"\n",
"grd2netCDF = \"Abyss_\" + str(dive) + \"_navadj_\" + str(sr) + \"m_netCDF\"\n",
"grd3 = \"Abyss\" + str(dive) + \"_navadj2_\" + str(sr) + \"m\"\n",
"grd4 = \"Abyss\" + str(dive) + \"_navadj_shift_\" + str(sr) + \"m\"\n",
"grd1 = device + \"_\" + str(dive) + \"_raw_\" + str(sr) + \"m\"\n",
"grd1nav = device + \"_\" + str(dive) + \"_raw_nav\"\n",
"grd2arcAscii = device + \"_\" + str(dive) + \"_navadj_\" + str(sr) + \"m_arcAscii\"\n",
"grd2netCDF = device + \"_\" + str(dive) + \"_navadj_\" + str(sr) + \"m_netCDF\"\n",
"grd3 = device + \"_\" + str(dive) + \"_navadj2_\" + str(sr) + \"m\"\n",
"grd4 = device + \"_\" + str(dive) + \"_navadj_shift_\" + str(sr) + \"m\"\n",
"\n",
"# define name of navadjust project (make sure this alings with what you enter in navadjust later)\n",
"navadjustProjectName = \"Abyss0250_navadj\""
......@@ -223,17 +230,79 @@
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"/media/jochen/Work/AUV_navadjust_4Jochen/Abyss0253\n",
"datalistp_0XXX.mb-1\n",
"20161214_173622p.mb88\r\n",
"20161214_173622pp.mb88\r\n",
"20161214_175151p.mb88\r\n",
"20161214_175151pp.mb88\r\n",
"20161214_180749p.mb88\r\n",
"20161214_180749pp.mb88\r\n",
"20161214_182409p.mb88\r\n",
"20161214_182409pp.mb88\r\n",
"20161214_184018p.mb88\r\n",
"20161214_184018pp.mb88\r\n",
"20161214_185640p.mb88\r\n",
"20161214_185640pp.mb88\r\n",
"20161214_191237p.mb88\r\n",
"20161214_191237pp.mb88\r\n",
"20161214_192807p.mb88\r\n",
"20161214_192807pp.mb88\r\n",
"20161214_194327p.mb88\r\n",
"20161214_194327pp.mb88\r\n",
"20161214_195900p.mb88\r\n",
"20161214_195900pp.mb88\r\n",
"20161214_201443p.mb88\r\n",
"20161214_201443pp.mb88\r\n",
"20161214_203113p.mb88\r\n",
"20161214_203113pp.mb88\r\n",
"20161214_204754p.mb88\r\n",
"20161214_204754pp.mb88\r\n",
"20161214_210432p.mb88\r\n",
"20161214_210432pp.mb88\r\n",
"20161214_212047p.mb88\r\n",
"20161214_212047pp.mb88\r\n",
"20161214_213715p.mb88\r\n",
"20161214_213715pp.mb88\r\n",
"20161214_215350p.mb88\r\n",
"20161214_215350pp.mb88\r\n",
"20161214_221009p.mb88\r\n",
"20161214_221009pp.mb88\r\n",
"20161214_222633p.mb88\r\n",
"20161214_222633pp.mb88\r\n",
"20161214_224242p.mb88\r\n",
"20161214_224242pp.mb88\r\n",
"20161214_225915p.mb88\r\n",
"20161214_225915pp.mb88\r\n",
"20161214_231534p.mb88\r\n",
"20161214_231534pp.mb88\r\n",
"20161214_233155p.mb88\r\n",
"20161214_233155pp.mb88\r\n",
"20161214_234754p.mb88\r\n",
"20161214_234754pp.mb88\r\n",
"20161215_000427p.mb88\r\n",
"20161215_000427pp.mb88\r\n",
"20161215_002123p.mb88\r\n",
"20161215_002123pp.mb88\r\n",
"20161215_003810p.mb88\r\n",
"20161215_003810pp.mb88\r\n",
"20161215_005518p.mb88\r\n",
"20161215_005518pp.mb88\r\n"
]
}
],
"source": [
"%cd $rootpath\n",
"print (datalistp)\n",
"\n",
"# Create datalist of preprocessed files\n",
"!ls -1 *p.mb88 > $datalistp"
"searchString = \"*p\" + file_ending\n",
"!ls -1 $searchString > $datalistp"
]
},
{
......@@ -360,7 +429,8 @@
"outputs": [],
"source": [
"%cd $rootpath\n",
"!ls -1 *pp.mb88 > $datalistpp"
"searchString_pp = \"*pp\" + file_ending\n",
"!ls -1 $searchString_pp > $datalistpp"
]
},
{
......@@ -602,7 +672,8 @@
"source": [
"# Create new datalist --> neccessary for merging project\n",
"%cd $rootpath\n",
"!ls -1 *ppp.mb88 > $datalistppp\n",
"searchString_ppp = \"*ppp\" + file_ending\n",
"!ls -1 $searchString_ppp > $datalistppp\n",
"\n",
"#set name for plot\n",
"navadjustPlotShift = navadjustProjectName + \"_shift\"\n",
......@@ -631,7 +702,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 11,
"metadata": {},
"outputs": [
{
......@@ -639,14 +710,33 @@
"output_type": "stream",
"text": [
"/media/jochen/Work/AUV_navadjust_4Jochen/Abyss0253\n",
"/media/jochen/Work/AUV_navadjust_4Jochen/Abyss0253\n",
"mkdir: cannot create directory ‘/media/jochen/Work/AUV_navadjust_4Jochen/Abyss0253/export’: File exists\n"
"mkdir: cannot create directory ‘/media/jochen/Work/AUV_navadjust_4Jochen/Abyss0253/export’: File exists\n",
"ls: cannot access '*ppp.mb88': No such file or directory\n",
"cp: missing file operand\n",
"Try 'cp --help' for more information.\n",
"cp: cannot stat 'Abyss_0XXX_raw_3m.asc': No such file or directory\n",
"cp: cannot stat 'Abyss_0XXX_navadj_3m_arcAscii.asc': No such file or directory\n",
"cp: cannot stat 'Abyss_0XXX_navadj2_3m.asc': No such file or directory\n",
"cp: cannot stat 'Abyss_0XXX_navadj_shift_3m.asc': No such file or directory\n",
"cp: cannot stat 'Abyss0250_navadj.dir': No such file or directory\n",
"cp: cannot stat 'Abyss0250_navadj.nvh': No such file or directory\n",
"\n",
"Unable to open data list file: datalist.mb-1\n",
"\n",
"Program <MBLIST> Terminated\n",
"\n",
"Unable to open data list file: datalist.mb-1\n",
"\n",
"Program <mbnavlist> Terminated\n",
"\n",
"Unable to open data list file: datalist.mb-1\n",
"\n",
"Program <mbnavlist> Terminated\n"
]
}
],
"source": [
"%cd $rootpath\n",
"!pwd\n",
"\n",
"#define export folder path\n",
"exportpath = rootpath + \"/export\"\n",
......@@ -655,9 +745,16 @@
"!mkdir $exportpath\n",
"\n",
"#export ppp files\n",
"!ls -1 *ppp.mb88 | xargs cp -t $exportpath\n",
"searchString_ppp = \"*ppp\" + file_ending\n",
"!ls -1 $searchString_ppp | xargs cp -t $exportpath\n",
"\n",
"#export grids\n",
"grd1File = grd1 + \".asc\"\n",
"!cp $grd1File $exportpath\n",
"grd2File = grd2arcAscii + \".asc\"\n",
"!cp $grd2File $exportpath\n",
"grd3File = grd3 + \".asc\"\n",
"!cp $grd3File $exportpath\n",
"grd4File = grd4 + \".asc\"\n",
"!cp $grd4File $exportpath\n",
"\n",
......@@ -667,30 +764,18 @@
"!cp -a $dirName $exportpath\n",
"#file .nvh\n",
"nvhName = navadjustProjectName + \".nvh\"\n",
"!cp $nvhName $exportpath\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"!mblist -Idatalist.mb-1 -D3 > Abyss0XXX_renav-soundings.xyz"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"!mbnavlist -Idatalist.mb-1 -OXYc >> Abyss0XXX_renav-vehicletrack.xyz\n",
"!mbnavlist -Idatalist.mb-1 -OJXYc >> Abyss0XXX_renav-vehicletrack+time.xyz ## for editing in Qimera"
"!cp $nvhName $exportpath\n",
"\n",
"#export lists\n",
"mblist_name = exportpath + \"/\" + device + \"_\" + dive + \"_renav-soundings.xyz\"\n",
"mbnavlist_name = exportpath + \"/\" + device + \"_\" + dive + \"_renav-vehicletrack.xyz\"\n",
"mbnavlist_time_name = exportpath + \"/\" + device + \"_\" + dive + \"_renav-vehicletrack_time.xyz\"\n",
"!mblist -Idatalist.mb-1 -D3 > $mblist_name\n",
"!mbnavlist -Idatalist.mb-1 -OXYc > $mbnavlist_name\n",
"!mbnavlist -Idatalist.mb-1 -OJXYc > $mbnavlist_time_name ## for editing in Qimera\n",
"\n",
"#save jupyter notebook\n",
"!cp $notebook $exportpath\n"
]
},
{
......@@ -722,9 +807,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": []
}
......@@ -732,21 +815,21 @@
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 2",
"language": "python",
"name": "python3"
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.1"
"pygments_lexer": "ipython2",
"version": "2.7.12"
}
},
"nbformat": 4,
......
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